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package jalview.gui; |
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import jalview.bin.Cache; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.ImageExporter.ImageWriterI; |
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import jalview.gui.StructureViewer.ViewerType; |
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import jalview.structures.models.AAStructureBindingModel; |
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import jalview.util.BrowserLauncher; |
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import jalview.util.ImageMaker; |
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import jalview.util.MessageManager; |
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import jalview.util.Platform; |
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import jalview.ws.dbsources.Pdb; |
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import java.awt.BorderLayout; |
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import java.awt.Color; |
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import java.awt.Dimension; |
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import java.awt.Font; |
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import java.awt.Graphics; |
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import java.awt.Rectangle; |
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import java.awt.event.ActionEvent; |
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import java.io.File; |
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import java.util.ArrayList; |
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import java.util.List; |
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import java.util.Vector; |
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import javax.swing.JCheckBoxMenuItem; |
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import javax.swing.JPanel; |
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import javax.swing.JSplitPane; |
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import javax.swing.SwingUtilities; |
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import javax.swing.event.InternalFrameAdapter; |
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import javax.swing.event.InternalFrameEvent; |
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| 57.3% |
Uncovered Elements: 123 (288) |
Complexity: 70 |
Complexity Density: 0.35 |
|
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public class AppJmol extends StructureViewerBase |
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{ |
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private static final int JMOL_LOAD_TIMEOUT = 20000; |
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private static final String SPACE = " "; |
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private static final String QUOTE = "\""; |
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AppJmolBinding jmb; |
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JPanel scriptWindow; |
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JSplitPane splitPane; |
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RenderPanel renderPanel; |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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@param |
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| 67.7% |
Uncovered Elements: 10 (31) |
Complexity: 6 |
Complexity Density: 0.26 |
|
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public AppJmol(String[] files, String[] ids, SequenceI[][] seqs,... |
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AlignmentPanel ap, boolean usetoColour, boolean useToAlign, |
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boolean leaveColouringToJmol, String loadStatus, Rectangle bounds, |
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String viewid) |
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{ |
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PDBEntry[] pdbentrys = new PDBEntry[files.length]; |
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for (int i = 0; i < pdbentrys.length; i++) |
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{ |
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PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, |
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files[i]); |
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pdbentrys[i] = pdbentry; |
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} |
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jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), |
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pdbentrys, seqs, null); |
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jmb.setLoadingFromArchive(true); |
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addAlignmentPanel(ap); |
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if (useToAlign) |
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{ |
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useAlignmentPanelForSuperposition(ap); |
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} |
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initMenus(); |
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if (leaveColouringToJmol || !usetoColour) |
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{ |
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jmb.setColourBySequence(false); |
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seqColour.setSelected(false); |
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viewerColour.setSelected(true); |
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} |
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else if (usetoColour) |
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{ |
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useAlignmentPanelForColourbyseq(ap); |
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jmb.setColourBySequence(true); |
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seqColour.setSelected(true); |
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viewerColour.setSelected(false); |
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} |
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this.setBounds(bounds); |
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setViewId(viewid); |
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this.addInternalFrameListener(new InternalFrameAdapter() |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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8 |
@Override... |
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public void internalFrameClosing( |
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InternalFrameEvent internalFrameEvent) |
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{ |
140 |
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closeViewer(false); |
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} |
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}); |
143 |
8 |
initJmol(loadStatus); |
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} |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
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10 |
@Override... |
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protected void initMenus() |
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{ |
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super.initMenus(); |
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viewerActionMenu.setText(MessageManager.getString("label.jmol")); |
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viewerColour |
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.setText(MessageManager.getString("label.colour_with_jmol")); |
155 |
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viewerColour.setToolTipText(MessageManager |
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.getString("label.let_jmol_manage_structure_colours")); |
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} |
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IProgressIndicator progressBar = null; |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@Override... |
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protected IProgressIndicator getIProgressIndicator() |
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{ |
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return progressBar; |
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} |
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@param |
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@param |
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@param |
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@param |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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2 |
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,... |
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final AlignmentPanel ap) |
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{ |
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progressBar = ap.alignFrame; |
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|
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openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry }, |
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new SequenceI[][] |
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{ seq }); |
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} |
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| 100% |
Uncovered Elements: 0 (13) |
Complexity: 1 |
Complexity Density: 0.08 |
|
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2 |
private void openNewJmol(AlignmentPanel ap, boolean alignAdded,... |
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PDBEntry[] pdbentrys, |
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SequenceI[][] seqs) |
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{ |
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2 |
progressBar = ap.alignFrame; |
190 |
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jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), |
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pdbentrys, seqs, null); |
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addAlignmentPanel(ap); |
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useAlignmentPanelForColourbyseq(ap); |
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|
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2 |
alignAddedStructures = alignAdded; |
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2 |
useAlignmentPanelForSuperposition(ap); |
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|
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2 |
jmb.setColourBySequence(true); |
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2 |
setSize(400, 400); |
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initMenus(); |
201 |
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addingStructures = false; |
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2 |
worker = new Thread(this); |
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2 |
worker.start(); |
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|
205 |
2 |
this.addInternalFrameListener(new InternalFrameAdapter() |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
207 |
2 |
@Override... |
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public void internalFrameClosing( |
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InternalFrameEvent internalFrameEvent) |
210 |
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{ |
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2 |
closeViewer(false); |
212 |
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} |
213 |
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}); |
214 |
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215 |
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} |
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217 |
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218 |
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219 |
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@param |
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@param |
223 |
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224 |
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@param |
225 |
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@param |
226 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
227 |
0 |
public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,... |
228 |
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SequenceI[][] seqs) |
229 |
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{ |
230 |
0 |
openNewJmol(ap, alignAdded, pe, seqs); |
231 |
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} |
232 |
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|
233 |
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| 85% |
Uncovered Elements: 3 (20) |
Complexity: 3 |
Complexity Density: 0.19 |
|
234 |
10 |
void initJmol(String command)... |
235 |
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{ |
236 |
10 |
jmb.setFinishedInit(false); |
237 |
10 |
renderPanel = new RenderPanel(); |
238 |
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|
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|
240 |
10 |
this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); |
241 |
10 |
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(), |
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getBounds().width, getBounds().height); |
243 |
10 |
if (scriptWindow == null) |
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{ |
245 |
10 |
BorderLayout bl = new BorderLayout(); |
246 |
10 |
bl.setHgap(0); |
247 |
10 |
bl.setVgap(0); |
248 |
10 |
scriptWindow = new JPanel(bl); |
249 |
10 |
scriptWindow.setVisible(false); |
250 |
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} |
251 |
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|
252 |
10 |
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, |
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null); |
254 |
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|
255 |
10 |
if (command == null) |
256 |
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{ |
257 |
0 |
command = ""; |
258 |
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} |
259 |
10 |
jmb.evalStateCommand(command); |
260 |
10 |
jmb.evalStateCommand("set hoverDelay=0.1"); |
261 |
10 |
jmb.setFinishedInit(true); |
262 |
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} |
263 |
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| 0% |
Uncovered Elements: 13 (13) |
Complexity: 4 |
Complexity Density: 0.57 |
|
264 |
0 |
@Override... |
265 |
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void showSelectedChains() |
266 |
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{ |
267 |
0 |
Vector<String> toshow = new Vector<>(); |
268 |
0 |
for (int i = 0; i < chainMenu.getItemCount(); i++) |
269 |
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{ |
270 |
0 |
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) |
271 |
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{ |
272 |
0 |
JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); |
273 |
0 |
if (item.isSelected()) |
274 |
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{ |
275 |
0 |
toshow.addElement(item.getText()); |
276 |
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} |
277 |
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} |
278 |
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} |
279 |
0 |
jmb.centerViewer(toshow); |
280 |
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} |
281 |
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
282 |
11 |
@Override... |
283 |
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public void closeViewer(boolean closeExternalViewer) |
284 |
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{ |
285 |
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|
286 |
11 |
if (jmb != null) |
287 |
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{ |
288 |
10 |
jmb.closeViewer(); |
289 |
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} |
290 |
11 |
setAlignmentPanel(null); |
291 |
11 |
_aps.clear(); |
292 |
11 |
_alignwith.clear(); |
293 |
11 |
_colourwith.clear(); |
294 |
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|
295 |
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|
296 |
11 |
jmb = null; |
297 |
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} |
298 |
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| 88.9% |
Uncovered Elements: 1 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
299 |
3 |
@Override... |
300 |
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public void run() |
301 |
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{ |
302 |
3 |
_started = true; |
303 |
3 |
try |
304 |
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{ |
305 |
3 |
List<String> files = fetchPdbFiles(); |
306 |
3 |
if (files.size() > 0) |
307 |
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{ |
308 |
3 |
showFilesInViewer(files); |
309 |
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} |
310 |
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} finally |
311 |
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{ |
312 |
3 |
_started = false; |
313 |
3 |
worker = null; |
314 |
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} |
315 |
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} |
316 |
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317 |
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318 |
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319 |
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320 |
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321 |
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@param |
322 |
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|
323 |
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| 59.3% |
Uncovered Elements: 22 (54) |
Complexity: 13 |
Complexity Density: 0.3 |
|
324 |
3 |
void showFilesInViewer(List<String> files)... |
325 |
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{ |
326 |
3 |
long lastnotify = jmb.getLoadNotifiesHandled(); |
327 |
3 |
StringBuilder fileList = new StringBuilder(); |
328 |
3 |
for (String s : files) |
329 |
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{ |
330 |
3 |
fileList.append(SPACE).append(QUOTE) |
331 |
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.append(Platform.escapeString(s)).append(QUOTE); |
332 |
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} |
333 |
3 |
String filesString = fileList.toString(); |
334 |
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|
335 |
3 |
if (!addingStructures) |
336 |
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{ |
337 |
2 |
try |
338 |
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{ |
339 |
2 |
initJmol("load FILES " + filesString); |
340 |
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} catch (OutOfMemoryError oomerror) |
341 |
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{ |
342 |
0 |
new OOMWarning("When trying to open the Jmol viewer!", oomerror); |
343 |
0 |
Cache.log.debug("File locations are " + filesString); |
344 |
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} catch (Exception ex) |
345 |
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{ |
346 |
0 |
Cache.log.error("Couldn't open Jmol viewer!", ex); |
347 |
0 |
ex.printStackTrace(); |
348 |
0 |
return; |
349 |
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} |
350 |
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} |
351 |
|
else |
352 |
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{ |
353 |
1 |
StringBuilder cmd = new StringBuilder(); |
354 |
1 |
cmd.append("loadingJalviewdata=true\nload APPEND "); |
355 |
1 |
cmd.append(filesString); |
356 |
1 |
cmd.append("\nloadingJalviewdata=null"); |
357 |
1 |
final String command = cmd.toString(); |
358 |
1 |
lastnotify = jmb.getLoadNotifiesHandled(); |
359 |
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|
360 |
1 |
try |
361 |
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{ |
362 |
1 |
jmb.evalStateCommand(command); |
363 |
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} catch (OutOfMemoryError oomerror) |
364 |
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{ |
365 |
0 |
new OOMWarning("When trying to add structures to the Jmol viewer!", |
366 |
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oomerror); |
367 |
0 |
Cache.log.debug("File locations are " + filesString); |
368 |
0 |
return; |
369 |
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} catch (Exception ex) |
370 |
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{ |
371 |
0 |
Cache.log.error("Couldn't add files to Jmol viewer!", ex); |
372 |
0 |
ex.printStackTrace(); |
373 |
0 |
return; |
374 |
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} |
375 |
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} |
376 |
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|
377 |
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|
378 |
3 |
int waitMax = JMOL_LOAD_TIMEOUT; |
379 |
3 |
int waitFor = 35; |
380 |
3 |
int waitTotal = 0; |
381 |
3 |
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() |
382 |
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: !(jmb.isFinishedInit() && jmb.getStructureFiles() != null |
383 |
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&& jmb.getStructureFiles().length == files.size())) |
384 |
|
{ |
385 |
0 |
try |
386 |
|
{ |
387 |
0 |
Cache.log.debug("Waiting around for jmb notify."); |
388 |
0 |
Thread.sleep(waitFor); |
389 |
0 |
waitTotal += waitFor; |
390 |
|
} catch (Exception e) |
391 |
|
{ |
392 |
|
} |
393 |
0 |
if (waitTotal > waitMax) |
394 |
|
{ |
395 |
0 |
System.err.println("Timed out waiting for Jmol to load files after " |
396 |
|
+ waitTotal + "ms"); |
397 |
|
|
398 |
|
|
399 |
|
|
400 |
0 |
jmb.getStructureFiles(); |
401 |
0 |
break; |
402 |
|
} |
403 |
|
} |
404 |
|
|
405 |
|
|
406 |
3 |
for (AlignmentPanel ap : _colourwith) |
407 |
|
{ |
408 |
3 |
jmb.updateColours(ap); |
409 |
|
} |
410 |
|
|
411 |
3 |
if (alignAddedStructures) |
412 |
|
{ |
413 |
1 |
alignAddedStructures(); |
414 |
|
} |
415 |
3 |
addingStructures = false; |
416 |
|
} |
417 |
|
|
418 |
|
|
419 |
|
|
420 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
421 |
1 |
void alignAddedStructures()... |
422 |
|
{ |
423 |
1 |
javax.swing.SwingUtilities.invokeLater(new Runnable() |
424 |
|
{ |
|
|
| 37.5% |
Uncovered Elements: 5 (8) |
Complexity: 3 |
Complexity Density: 0.5 |
|
425 |
1 |
@Override... |
426 |
|
public void run() |
427 |
|
{ |
428 |
1 |
if (jmb.viewer.isScriptExecuting()) |
429 |
|
{ |
430 |
0 |
SwingUtilities.invokeLater(this); |
431 |
0 |
try |
432 |
|
{ |
433 |
0 |
Thread.sleep(5); |
434 |
|
} catch (InterruptedException q) |
435 |
|
{ |
436 |
|
} |
437 |
0 |
return; |
438 |
|
} |
439 |
|
else |
440 |
|
{ |
441 |
1 |
alignStructs_withAllAlignPanels(); |
442 |
|
} |
443 |
|
} |
444 |
|
}); |
445 |
|
|
446 |
|
} |
447 |
|
|
448 |
|
|
449 |
|
|
450 |
|
|
451 |
|
|
452 |
|
|
453 |
|
|
454 |
|
@return |
455 |
|
|
|
|
| 51.7% |
Uncovered Elements: 29 (60) |
Complexity: 16 |
Complexity Density: 0.4 |
|
456 |
3 |
List<String> fetchPdbFiles()... |
457 |
|
{ |
458 |
|
|
459 |
3 |
StringBuilder errormsgs = new StringBuilder(); |
460 |
|
|
461 |
3 |
List<String> files = new ArrayList<>(); |
462 |
3 |
String pdbid = ""; |
463 |
3 |
try |
464 |
|
{ |
465 |
3 |
String[] filesInViewer = jmb.getStructureFiles(); |
466 |
|
|
467 |
|
|
468 |
3 |
Pdb pdbclient = new Pdb(); |
469 |
7 |
for (int pi = 0; pi < jmb.getPdbCount(); pi++) |
470 |
|
{ |
471 |
4 |
String file = jmb.getPdbEntry(pi).getFile(); |
472 |
4 |
if (file == null) |
473 |
|
{ |
474 |
|
|
475 |
|
|
476 |
0 |
AlignmentI pdbseq = null; |
477 |
0 |
pdbid = jmb.getPdbEntry(pi).getId(); |
478 |
0 |
long hdl = pdbid.hashCode() - System.currentTimeMillis(); |
479 |
0 |
if (progressBar != null) |
480 |
|
{ |
481 |
0 |
progressBar.setProgressBar(MessageManager |
482 |
|
.formatMessage("status.fetching_pdb", new String[] |
483 |
|
{ pdbid }), hdl); |
484 |
|
} |
485 |
0 |
try |
486 |
|
{ |
487 |
0 |
pdbseq = pdbclient.getSequenceRecords(pdbid); |
488 |
|
} catch (OutOfMemoryError oomerror) |
489 |
|
{ |
490 |
0 |
new OOMWarning("Retrieving PDB id " + pdbid, oomerror); |
491 |
|
} catch (Exception ex) |
492 |
|
{ |
493 |
0 |
ex.printStackTrace(); |
494 |
0 |
errormsgs.append("'").append(pdbid).append("'"); |
495 |
|
} finally |
496 |
|
{ |
497 |
0 |
if (progressBar != null) |
498 |
|
{ |
499 |
0 |
progressBar.setProgressBar( |
500 |
|
MessageManager.getString("label.state_completed"), |
501 |
|
hdl); |
502 |
|
} |
503 |
|
} |
504 |
0 |
if (pdbseq != null) |
505 |
|
{ |
506 |
|
|
507 |
|
|
508 |
0 |
file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries() |
509 |
|
.elementAt(0).getFile()).getAbsolutePath(); |
510 |
0 |
jmb.getPdbEntry(pi).setFile(file); |
511 |
0 |
files.add(file); |
512 |
|
} |
513 |
|
else |
514 |
|
{ |
515 |
0 |
errormsgs.append("'").append(pdbid).append("' "); |
516 |
|
} |
517 |
|
} |
518 |
|
else |
519 |
|
{ |
520 |
4 |
if (filesInViewer != null && filesInViewer.length > 0) |
521 |
|
{ |
522 |
2 |
addingStructures = true; |
523 |
3 |
for (int c = 0; c < filesInViewer.length; c++) |
524 |
|
{ |
525 |
2 |
if (filesInViewer[c].equals(file)) |
526 |
|
{ |
527 |
1 |
file = null; |
528 |
1 |
break; |
529 |
|
} |
530 |
|
} |
531 |
|
} |
532 |
4 |
if (file != null) |
533 |
|
{ |
534 |
3 |
files.add(file); |
535 |
|
} |
536 |
|
} |
537 |
|
} |
538 |
|
} catch (OutOfMemoryError oomerror) |
539 |
|
{ |
540 |
0 |
new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); |
541 |
|
} catch (Exception ex) |
542 |
|
{ |
543 |
0 |
ex.printStackTrace(); |
544 |
0 |
errormsgs.append("When retrieving pdbfiles : current was: '") |
545 |
|
.append(pdbid).append("'"); |
546 |
|
} |
547 |
3 |
if (errormsgs.length() > 0) |
548 |
|
{ |
549 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
550 |
|
MessageManager.formatMessage( |
551 |
|
"label.pdb_entries_couldnt_be_retrieved", new String[] |
552 |
|
{ errormsgs.toString() }), |
553 |
|
MessageManager.getString("label.couldnt_load_file"), |
554 |
|
JvOptionPane.ERROR_MESSAGE); |
555 |
|
} |
556 |
3 |
return files; |
557 |
|
} |
558 |
|
|
559 |
|
|
560 |
|
|
561 |
|
|
562 |
|
|
563 |
|
|
564 |
|
@param |
565 |
|
|
|
|
| 0% |
Uncovered Elements: 6 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
|
566 |
0 |
public void makePDBImage(ImageMaker.TYPE type)... |
567 |
|
{ |
568 |
0 |
int width = getWidth(); |
569 |
0 |
int height = getHeight(); |
570 |
0 |
ImageWriterI writer = new ImageWriterI() |
571 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
572 |
0 |
@Override... |
573 |
|
public void exportImage(Graphics g) throws Exception |
574 |
|
{ |
575 |
0 |
jmb.viewer.renderScreenImage(g, width, height); |
576 |
|
} |
577 |
|
}; |
578 |
0 |
String view = MessageManager.getString("action.view").toLowerCase(); |
579 |
0 |
ImageExporter exporter = new ImageExporter(writer, |
580 |
|
jmb.getIProgressIndicator(), type, getTitle()); |
581 |
0 |
exporter.doExport(null, this, width, height, view); |
582 |
|
} |
583 |
|
|
|
|
| 0% |
Uncovered Elements: 2 (2) |
Complexity: 2 |
Complexity Density: 1 |
|
584 |
0 |
@Override... |
585 |
|
public void showHelp_actionPerformed(ActionEvent actionEvent) |
586 |
|
{ |
587 |
0 |
try |
588 |
|
{ |
589 |
0 |
BrowserLauncher |
590 |
|
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); |
591 |
|
} catch (Exception ex) |
592 |
|
{ |
593 |
|
} |
594 |
|
} |
595 |
|
|
|
|
| 0% |
Uncovered Elements: 21 (21) |
Complexity: 4 |
Complexity Density: 0.27 |
|
596 |
0 |
public void showConsole(boolean showConsole)... |
597 |
|
{ |
598 |
|
|
599 |
0 |
if (showConsole) |
600 |
|
{ |
601 |
0 |
if (splitPane == null) |
602 |
|
{ |
603 |
0 |
splitPane = new JSplitPane(JSplitPane.VERTICAL_SPLIT); |
604 |
0 |
splitPane.setTopComponent(renderPanel); |
605 |
0 |
splitPane.setBottomComponent(scriptWindow); |
606 |
0 |
this.getContentPane().add(splitPane, BorderLayout.CENTER); |
607 |
0 |
splitPane.setDividerLocation(getHeight() - 200); |
608 |
0 |
scriptWindow.setVisible(true); |
609 |
0 |
scriptWindow.validate(); |
610 |
0 |
splitPane.validate(); |
611 |
|
} |
612 |
|
|
613 |
|
} |
614 |
|
else |
615 |
|
{ |
616 |
0 |
if (splitPane != null) |
617 |
|
{ |
618 |
0 |
splitPane.setVisible(false); |
619 |
|
} |
620 |
|
|
621 |
0 |
splitPane = null; |
622 |
|
|
623 |
0 |
this.getContentPane().add(renderPanel, BorderLayout.CENTER); |
624 |
|
} |
625 |
|
|
626 |
0 |
validate(); |
627 |
|
} |
628 |
|
|
|
|
| 20.6% |
Uncovered Elements: 27 (34) |
Complexity: 10 |
Complexity Density: 0.43 |
|
629 |
|
class RenderPanel extends JPanel |
630 |
|
{ |
631 |
|
final Dimension currentSize = new Dimension(); |
632 |
|
|
|
|
| 18.2% |
Uncovered Elements: 27 (33) |
Complexity: 10 |
Complexity Density: 0.43 |
|
633 |
172 |
@Override... |
634 |
|
public void paintComponent(Graphics g) |
635 |
|
{ |
636 |
172 |
getSize(currentSize); |
637 |
|
|
638 |
172 |
if (jmb != null && jmb.hasFileLoadingError()) |
639 |
|
{ |
640 |
0 |
g.setColor(Color.black); |
641 |
0 |
g.fillRect(0, 0, currentSize.width, currentSize.height); |
642 |
0 |
g.setColor(Color.white); |
643 |
0 |
g.setFont(new Font("Verdana", Font.BOLD, 14)); |
644 |
0 |
g.drawString(MessageManager.getString("label.error_loading_file") |
645 |
|
+ "...", 20, currentSize.height / 2); |
646 |
0 |
StringBuffer sb = new StringBuffer(); |
647 |
0 |
int lines = 0; |
648 |
0 |
for (int e = 0; e < jmb.getPdbCount(); e++) |
649 |
|
{ |
650 |
0 |
sb.append(jmb.getPdbEntry(e).getId()); |
651 |
0 |
if (e < jmb.getPdbCount() - 1) |
652 |
|
{ |
653 |
0 |
sb.append(","); |
654 |
|
} |
655 |
|
|
656 |
0 |
if (e == jmb.getPdbCount() - 1 || sb.length() > 20) |
657 |
|
{ |
658 |
0 |
lines++; |
659 |
0 |
g.drawString(sb.toString(), 20, currentSize.height / 2 |
660 |
|
- lines * g.getFontMetrics().getHeight()); |
661 |
|
} |
662 |
|
} |
663 |
|
} |
664 |
172 |
else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit()) |
665 |
|
{ |
666 |
0 |
g.setColor(Color.black); |
667 |
0 |
g.fillRect(0, 0, currentSize.width, currentSize.height); |
668 |
0 |
g.setColor(Color.white); |
669 |
0 |
g.setFont(new Font("Verdana", Font.BOLD, 14)); |
670 |
0 |
g.drawString(MessageManager.getString("label.retrieving_pdb_data"), |
671 |
|
20, currentSize.height / 2); |
672 |
|
} |
673 |
|
else |
674 |
|
{ |
675 |
172 |
jmb.viewer.renderScreenImage(g, currentSize.width, |
676 |
|
currentSize.height); |
677 |
|
} |
678 |
|
} |
679 |
|
} |
680 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
681 |
368 |
@Override... |
682 |
|
public AAStructureBindingModel getBinding() |
683 |
|
{ |
684 |
368 |
return this.jmb; |
685 |
|
} |
686 |
|
|
|
|
| 66.7% |
Uncovered Elements: 1 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
687 |
2 |
@Override... |
688 |
|
public String getStateInfo() |
689 |
|
{ |
690 |
2 |
return jmb == null ? null : jmb.viewer.getStateInfo(); |
691 |
|
} |
692 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
693 |
20 |
@Override... |
694 |
|
public ViewerType getViewerType() |
695 |
|
{ |
696 |
20 |
return ViewerType.JMOL; |
697 |
|
} |
698 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
699 |
11 |
@Override... |
700 |
|
protected String getViewerName() |
701 |
|
{ |
702 |
11 |
return "Jmol"; |
703 |
|
} |
704 |
|
} |